Large-scale reconstruction of chromatin structures of maize temperate and tropical inbred lines

Lei Tian, Lixia Ku, Zan Yuan, Cuiling Wang, Huihui Su, Shunxi Wang, Xiaoheng Song, Dandan Dou, Zhenzhen Ren, Jinsheng Lai, Tao Liu, Chunguang Du, Yanhui Chen, Tao Liu, Chunguang Du

Research output: Contribution to journalArticlepeer-review

Abstract

Maize is a model plant species often used for genetics and genomics research because of its genetic diversity. There are prominent morphological, genetic, and epigenetic variations between tropical and temperate maize lines. However, the genome-wide chromatin conformations of these two maize types remain unexplored. We applied a Hi-C approach to compare the genome-wide chromatin interactions between temperate inbred line D132 and tropical line CML288. A reconstructed maize three-dimensional genome model revealed the spatial segregation of the global A and B compartments. The A compartments contain enriched genes and active epigenome marks, whereas the B compartments are gene-poor, transcriptionally silent chromatin regions. Whole-genome analyses indicated that the global A compartment content of CML288 was 3.12% lower than that of D132. Additionally, global and A/B sub-compartments were associated with differential gene expression and epigenetic changes between two inbred lines. About 25.3% of topologically associating domains (TADs) were determined to be associated with complex domain-level modifications that induced transcriptional changes, indicative of a large-scale reorganization of chromatin structures between the inbred maize lines. Furthermore, differences in chromatin interactions between the two lines correlated with epigenetic changes. These findings provide a solid foundation for the wider plant community to further investigate the genome-wide chromatin structures in other plant species.

Original languageEnglish
Pages (from-to)3582-3596
Number of pages15
JournalJournal of Experimental Botany
Volume72
Issue number10
DOIs
StatePublished - 4 May 2021

Keywords

  • Chromatin structures
  • epigenetic change
  • Hi-C
  • large-scale reconstruction
  • maize germplasm
  • morphology
  • transcriptional regulation

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